Visual Programming for Modeling and Simulation of Biomolecular Regulatory Networks

Rajeev Alur, University of Pennsylvania
Calin Belta, University of Pennsylvania
Franjo Ivancic, University of Pennsylvania
R. Vijay Kumar, University of Pennsylvania
Harvey Rubin, University of Pennsylvania
Jonathan Schug, University of Pennsylvania
Oleg Sokolsky, University of Pennsylvania
Jonathan Webb, BBN Technologies

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Postprint version. Published in Lecture Notes in Computer Science, Volume 2552, High Performance Computing - HiPC 2002, pages 702-712.
Publisher URL: http://www.springerlink.com/link.asp?id=gt7d938fl0y8qpj0

Abstract

In this paper we introduce our new tool BIOSKETCHPAD that allows visual programming and modeling of biological regulatory networks. The tool allows biologists to create dynamic models of networks using a menu of icons, arrows, and pop-up menus, and translates the input model into CHARON, a modeling language for modular design of interacting multi-agent hybrid systems. Hybrid systems are systems that are characterized by continuous as well as discrete dynamics. Once a CHARON model of the underlying system is generated, we are able to exploit the various analysis capabilities of the CHARON toolkit, including simulation and reachability analysis. We illustrate the advantages of this approach using a case study concerning the regulation of bioluminescence in a marine bacterium.